Alternating Possibilities
by Gesser87
Summary: During the 15th Angel, an event occurs that sets in motion changes that will have a major impact on the final outcome.
1. Chapter 1

Alternating Possibilities

Alternating Possibilities

By Gesser87

Disclaimer: Neon Genesis Evangelion and all its characters, concepts, etc., belong to Gainax.

Chapter 1 – The Arrival

"Hold your position and await further orders." Misatos's voice came over the comm system, as Asuka patiently waited for the targeting indicators to align.

As she looked at the Angel's image in her visor, the pain returned. The sharp pain her shoulders that reminded her of her last fight with an Angel.

She could still remember it's face; that looked as if it was laughing at her while it sliced of her arms.

Her angry growl, as she tried to ram into the Angel.

The feeling of it's sharp arms slicing thru her neck and the sudden power down of her EVA.

The defeat itself was great shame for her, but what made her shame even worse was the fact that she was saved by Shinji. The coward that ran away and left them weakened to the attack, only to return later and prove his reputation as the 'Invincible Shinji'.

Since then her sync ratio has been steadily dropping and she knew that it was a matter of time before the Marduk Institute would find another pilot. A pilot that will replace her. The thought of loosing her EVA, the only thing left from her mother, made her blood boil.

'I won't lose to anyone .NOT TO SHINJI. NOT TO REI. NOT TO ANYONE.' She angrily thought, as she tightened her grip on the controls.

A lonely figure walked down the streets of Tokyo 3. He knew that something was going on, but didn't know what. All the signs in the street have changed and some kind of announcement was constantly played through the PA system.

'I should have bought that dictionary while I was at the airport.' He thought, as he started to have a bad feeling. He walked over to one of the massive buildings and leaned against it, dropping his back-pack by his side.

"Congratulations. Your easy-way-no-problem tactics have backfired. Again" He said to himself.

With the corner of his eye, he noticed a large, silver tube that made a great contrast against the monolith buildings. He turned around and saw that the tube belonged to a massive cannon that was held by a red giant. His mind was immediately devoid of any kind of thoughts as he watched the sight that was before him.

"What the….," was all he could say.

'TARGET OUT OF RANGE' The display flashed.

"Verdammt!" Asuka said, feeling tempted to smash the controls, but she managed to calm down and reset the sequence.

"Ma'am, there is a civilian close to Unit 02!" A technician's voice came over the comm. Misato immediately demanded to know how the civilian managed to get close to the Eva. But before she could finish her sentence, Asuka was blinded by the brightest light had ever seen. It only served to mask the hell the she was about to experience.

And then, it all began to come back to her, the images that she tried to forget.

A little girl running down the hallway, wanting to tell her mother the great news.

The girl's excitement of seeing her mother happy.

As the girl approached the door at the end of the hallway, Asuka knew what was about to happen. She wanted to close her eyes and run away from the horrible scene, but she couldn't do anything.

The girl slowly opened the door.

"Mutti, Ich habbe…" The girl stopped dead in her track as she saw a body hanging from the ceiling, accompanied by a small doll.

"GET OUT OF MY HEAD!!" Asuka screamed, hoping that it will drive the images away. But it didn't help.

"Abnormal patterns in psychograph. Mental contamination will commence soon." Maya Ibuki almost said, reading the data that were displayed on her terminal.

Misato was almost frozen by this sudden turn of events. She had to do something and save Asuka from the Angel's attack, but the only thing she could think of were Asuka's screams of pain. It brought back the memories of the Second Impact, when her father died protecting her.

"Rei is in position. She'll be able to fire in 40 seconds." Aoba said, waking Misato out of her trance.

"ANOTHER FIELD DETECTED!" Maya yelled as the screen of her terminal was flashed in a new color.

"Another AT field?" Misato said, hoping that the situation won't make a turn for the worse.

"No, it's not an AT field." The technician answered. "It's constantly altering between the orange and an unidentified pattern."

"Asuka's psychograph is returning to normal." Ryuga said with amazement.

"Charging cycle is at 68. Rei's targeting computer has confirmed lock-on." Aoba announced.

Arael, the Angel of Birds, was finishing of one of the lilim's guardian. She could feel its mind weaken under her assault.

'Soon Adam, we will be one.' she thought.

She could feel another one of the guardians approaching, but she didn't care. She knew that as long as she kept her distance, she would be safe from their weapons. Suddenly, her mind was assaulted with images.

The Second Impact, the day when Adam was lost.

Adam and his horrifying scream of pain.

Her brothers and sisters; that have died by the hand of lilims.

She couldn't understand how it was possible to be attacked by her own attack. It couldn't have been one of her brethren. She thought that the lilim had something to do with this, but she knew that they weren't capable of doing something like this.

Before she found out her answer, she saw a large white ball heading in her direction.

And then, her whole world went black.

Inside the dark plug of an unpowered EVA, Asuka silently cried.

She could hear Misato's voice over the comm., but she didn't care. It was all over for her. From a couple of weeks, her replacement will arrive in a couple of days. She was now good as dead.

Suddenly, the plug was no longer cold. She opened her eyes and saw the plug was lighted, as if the EVA was still active.

She felt someone embracing her from behind. The grip was gentle, but firm. The warmth of the second person was almost intoxicating. She thought of the only one person that could give her this feeling.

"Kaji…" She managed to whisper his name.

"Sorry, but I'm not Kaji." Said a voice, much younger than the one she was expecting. She turned around, hoping that it was here mind playing tricks on her. She looked into his blue eyes. His face was that of the 14 year old boy with whom she shared the apartment. The sight of his simple face brought comfort to her. She tried to demand how he ended up in the plug and end up affect by the Angel, but Shinji placed his finger on her lips.

"It's alright, Asuka. You're safe." He said in a calm and comforting manner.

She began to think that this Shinji was maybe another image created by the angel, that would only hurt her even more once she lowered her guard.

As if sensing her doubts, Shinji placed his hand on the side of her face and gave her a smile.

"Don't worry, Asuka. I'll keep you safe, no matter what. I promise."

Asuka was taken back with what he said. It wasn't what he said, it was the way he said surprised her. There were no traces of insecurity or in his voice. As his warmth started to make her feel drowsy, she lowered her head and leaned against Shinji. He gently hugged her and gently stroked her hair.

"Shinji…" She quietly said, feeling completely intoxicated with his presence.

"ASUKA!!" Misato's screaming made Asuka look up. Instead of Shinji's face she was Misato's face on the screen. Shinji's presence and the warmth suddenly disappeared. She looked around the plug, trying to find Shinji.

"Are you alright?"

"Stay put. A retrieval team is on it's way."

With that, Asuka brought her knees to her chest and closed her eyes. Till the team arrived and opened the plug, she tried to recreate that feeling.

Minutes later….

A black car stopped in the middle of the deserted streets of Tokyo 3. Two agents, dressed in black suits, left the car, leaving a third one behind the wheel. They approached a man that was leaning against the wall, covering his face with his hands. One of them stepped forward.

"Sir, are you alright?" He asked. The man nodded in response.

"Sir, you will have to come with us." The agent said in a cold tone that bordered with giving an order.

"I haven't done anything." The man silently said, taking his hands of his face.

"Sir, you will have to come with us." The agent repeated, reaching for something at his waist.

The man immediately reacted to the agent's gesture and punched the agent right in the face. The second agent moved in grabbed the man's right hand, trying to flip him on the ground; but he was suddenly stopped by a sudden pain in his groin. He fell down on his knees a second before the man's fist made contact with his face.

"Sorry, brother." The man said to the unconscious agent. A strange sensation went down his back. It felt like gentle caressing and hard pulling at the same time.

Suddenly, he felt 2 sharp pricks on his back. Before he could turn around, he felt another set of sharp pricks, followed by an intense pain as the electric current contracted every muscle in his body. The pain lasted for several agonizing moments before the world around him began to spin and then faded to black.

The third agent waited for several moments to see if the target was unconscious. He walked slowly to the unconscious body, holstering his tranquilizer gun, and cuffed his hands. The sudden sound of a low groan made him twitch. He looked over his shoulder and saw that the second agent was trying to get on his feet. He walked over to his colleague and gave him a hand. The first one pushed him away and got up on his own. He slowly walked over to the unconscious man and gave the man a mighty kick in the ribs. Just as he was about to do it for a second time, his colleague pulled him away.

"We need him alive!"

The second agent walked away, mumbling something. That left his colleague with an uncomfortable task of carrying the unconscious bodies of his fellow agent and their target to the car.

After several minutes of trying, he managed put their target in the back seat of the car and drove of to NERV headquarters before the civilian populations returned to the streets.

Three days later…

Inside a dark, cavernous room; 12 dark monoliths surrounded 2 people that were at large desk.

"This was not a part of the scenario, Ikari." The first monolith said.

"Even though the Angel is destroyed and the damages to Unit 02 and it's pilot were minimal; there is the issue of the mysterious field that managed to protect Unit 02." The second monolith said.

"This was not written in the scrolls."

"It could affect our scenario."

As the monoliths went on with their discussion about the possible effects on the scenario, Gendo Ikari stood still and patiently observed them. This wasn't the first time that he was in this kind of situation. And it wasn't the first time that he managed to squirm his way out of it. The secret of it was patiently waiting for the members to run out of arguments. Which was happening right now.

"Yes. It's true that was not a part of the scenario but, it could work to our advantage."

"Go on." The first monolith said.

"We are presented with a great opportunity and you can't allow your blind faith in the scrolls to let it slip away. A field that is powerful enough to reflect the Angel's attack and send it back can have many useful applications."

"You don't even know what created the field or it's location."

"It has shown itself once, it will show itself again. It's a matter of time before it resurfaces."

"Very well, Ikari. You will be given funding to locate and capture this 'entity'. But remember what our true goals are."

The human figure nodded, seconds before the light under it disappeared.

"He is starting to act independently." One of the monoliths said.

"So far, his actions have been according to the scenario. If he begins to defy us, it will most likely affect all of our scenarios."

"Should we continue to trust him?"

"I leave that choice completely to you" A cheerful voice said.

"Who is this?" one of the monoliths demanded.

"Oh, how rude of me, i forgot to turn on the video scanner. Give me a second."

A couple of moments later, in the place where the commander and vice-commander of NERV stood, a figure appeared. Its form looked human, but it was entirely black except for the eyes that glowed with a dimmed yellow light.

"Now, let's get str-" Before he could finish his sentence, one of the monoliths cut it off.

"Who are you and how did you find us?"

The figure sighed and slumped it's shoulders.

"No matter how old some people get, they still show no manners when speaking to others."

"How did you found this channel?" Another monolith demanded.

"For someone that wants to keep their talks secret, your security codes are outdated. It didn't took much effort to find this channel and to decode it." With that, all monoliths became silent.

"As I was saying," the figure continued, "I have come across some information that could be useful to you, and you have the infrastructure that is necessary for some things that I would like in return for this information. I suggest that we trade."

"Are you serious? What kind of information do you have that we don't already posses?" The first monolith said in an arrogant tone.

"Watch your mouth, Lorenz Keel. I have more than enough information on you and your Instrumentality project to lock all of you up for good." The figures 'eyes' distorted, showing anger which was in total contrast with it's happy voice.

Sensing their fear, the figure decided to seize the opportunity. The shape of it's eyes returned to their normal shape.

"As a sign of good will" The figure began to move it's hands, as if it was trying to type something on an invisible keyboard.

"What is the meaning of this?" One of the monoliths spoke.

"Exactly what it means, NERV's latest acquisition. A pilot that is not only an adult, but also has military experiences." Its last statement caused and uproar amongst the monoliths, all the figure needed to do now was to deliver the finishing blow.

"Looks like you are going to have a hell of a time dealing with NERV from now on."

Mumbling and whispering filled the room as the monoliths discussed whether or not they should trust this figure. After several minutes of debating, the monoliths made their decision.

"Very well, You have proven yourself." The first monolith spoke. "How can we reach you?"

"Use this channel. You can reach me at any time you want."

"How do you wish to be referred as?"

The figure paused and assumed a thinking pose. It hummed a tune for several minutes, until it came up with its name.

"Call me Glados."

End of Chapter 1


	2. Chapter 2

Chapter 2: Newest Acquisition

Chapter 2: Newest Acquisition

By Gesser87

Disclaimer: Read the 1st chapter.

217

That number could mean anything.

A part of a phone number.

The ID number of one of the city buses.

The Number of a hotel room.

Or in his case, number of the hospital room in which he was "sheltered".

Even though the doctors and nurses told him that he could leave at any time, but the two armed guards in front of his room proved it wrong.

It has been two days since he woke up, and the closest thing to human interaction were the doctors and nurses that only came to either take every kind of sample from him or to analyze his experience of that "attack" before he was found by their thugs. The only thing positive in that was that they made the room look less spacious. The room itself was quite big, comparing to the other hospital rooms that he was in. It was big enough to have another bed. Or a large amount of medical devices in case if something horrible were to happen. That thought send a massive chill running down his spine.

'What the hell is going on here?' He thought.

His train of thought was brought to a sudden stop by the sound of the door opening. He turned around and instead of the usual sight of a doctor or a young nurse, there was a man standing at the door. He appeared to be around 50 or so years old, wearing some kind of uniform. What immediately got his attention were two thick folders that man was holding. Judging by this man's stance and the way he was looking at him, it became clear that he was no pencil-pusher. After a minute of staring into the man's eyes that were behind the orange tinted glasses, he decided to break the silence.

"Who the hell are you?"

"Mr. Mulligan, my name is Gendo Ikari." The man said in a calm manner.

Dr. Akagi took a long sip of her coffee as one of the nurses brought her a thick folder.

"Here are all of the records that we have on the patient." The nurse said as she handed over a thick folder. It was clear to the blond doctor that this nurse was new to this kind of work.

"Good." Dr. Akagi said as she took the folder. "Were any of the records of this patient divulged to anyone?"

"Ah… No. I followed the instructions that were given to me by Section 2." The nurse said, trying to look as professional as possible.

"Good. If anyone asks…."

"He was never here." The nurse finished.

The doctor nodded as she finished signing the last of the discharge papers. With that done, she did the only thing that relaxed her during her work time. Drinking coffee. The taste of the hospitals coffee wasn't strong enough in her opinion, but it was at least stronger than the kind in NERV's cafeteria. After several minutes of enjoying the coffee, the door of room 217 opened. She turned her head in that direction and saw the Commander leaving the room, while the "patient" was sitting on his bed, reading something from a folder. She could only imagine the things that Commander told him and the dilemma he was going through.

"Dr. Akagi," The Commander began as he approached the blond doctor, "I leave the rest to you." With that, he proceeded to one of the elevators.

'Leaving me with the dirty work, again?' She thought as she took another sip of the coffee. A couple of moments later, the door of the room 217 opened again and this time the "patient" emerged from it. Judging by the look in his eyes, it was clear to the doctor that the Commander managed to crush his spirit and make him join NERV.

"Where do I leave this?" He asked as he approached the receptionist.

"I'll take that." Dr. Akagi said as she approached him. She opened one of the folders to check if he signed the document. "Please follow me." Just as they were about to go to on of the elevators, he suddenly kissed the nurse on the cheek.

"Don't worry, honey. They aren't here because of the banging that we did last night." He said. As he followed the doctor to the elevator, the nurse's face was beat-red.

As the elevator began it's descent to the parking level, Dr. Akagi took a chance to silently study his face. She has seen his face on the pictures that were in the reports along with his description, but she never got the chance to see him in person. His face was very masculine, comparing to the gentle and almost feminine faces of most of her male co-workers. As she paid more attention to some of his features, she began to notice a resemblance with someone.

'If he had an unshaved face and long hair, he would almost look like Kaji.' She though. But then she remembered the way he died. Despite the popular belief that was amongst NERV's staff, Kaji's death saddened her. Even though he was lying and scheming against Commander and all, he was one of the few people that were nice to her regardless of her status or her origin.

"So," the man broke the silence, bringing the doctor out of her thoughts, "what exactly is my job description?"

"The details of your job will be given tomorrow." She said in a calm tone.

The man smirked at the doctor's statement. "Just like when I was in the army."

This surprised the doctor. She couldn't tell from his face if he was smirking because of something funny or if he was trying to cover his anger. "Mr. Mulligan, please try to understand our position. We….." She tried to justify the commander's actions, but she was cut off when the man placed his hand on her shoulder.

"Miss, I don't have anything against this organization or its work. But, I do despise the Commander and the method he used to 'persuade' me to join this organization."

"I see."

They remained silent for several moments, until the elevator arrived at the desired level. The elevator door opened, revealing an empty parking level. On the far end of it, there was a black SUV and 2 men in black suits standing by it.

"Follow me Mr. Mulligan." The doctor said.

"Please, call me Mark."

In an apartment on the other side of town, a purple haired woman took another large swig of her beverage of choice. Usually, it would bring her a massive feeling of satisfaction, but this wasn't the case. It has been 3 days since the Angel attack and she was concerned with its ramifications. It didn't bother her that she had to write down and sign a massive amount of reports regarding the damages that occurred to the city or that she had to listen to a two-hour long lecture from Dr. Akagi on how she unnecessarily endangered the life of a pilot. But what bothered her the most was the sudden change in behavior of one of her charges. Even thought the doctors explained to her that, due to the nature of the Angel's attack, there might be certain changes in behavior; that still didn't prepare her for the changes in Asuka's behavior. She was still acting like she owned the place and she was still calling Shinji and idiot and a pervert, but at a lesser degree. If she didn't know any better, she could swear that she was trying to be nice towards Shinji.

'Maybe she has finally decided to drop the "Alpha female" act.' She thought, but immediately dismissed it.

Knowing from the time she saw her in Germany and what was written in her record, Misato knew that Asuka's extremely competitive nature wouldn't allow that… But still, it would be nice if Asuka would stop that act, for at least one day.

Her thoughts were interrupted by the sudden sound of a car parking near the apartment building. She went onto the balcony and saw a black SUV in front of the building. She could clearly see a familiar blond woman and three men entering the building.

'What the hell is Ritsu doing here all of a sudden?' She thought.

The men in black accompanied him to the apartment. He looked behind to ask the blonde woman a little more details on his job, but he saw that she was entering one of the apartments. For a second he thought that she was going in to contact someone that was supposed to surveillance him, but he immediately discarded that thought.

'That would be a little too obvious.' He thought.

They suddenly stopped in front of a door. One of his escorts took a key out of his pocket and opened it.

"This will be your residence." The escort said. "We will arrive tomorrow at 0630 to escort you to NERV HQ."

Being born and raised in the western world, it was a little surprising for Mark to see a typical Japanese apartment.

'Spartan to the core.' He thought, as he surveyed the apartment. Even though the apartment was barely furnished, it was quite big. He guessed that a four member family could live here and still have extra space. After accidentally entering the bathroom and a large empty room, he finally found a room with a bed in it. He placed the backpack on the table that was near the bed and opened it. What immediately caught his eye was the way things were arranged in his backpack. Or more precise, the way things were piled up inside the backpack.

"At least you could have tried to cover up the fact that you went through my stuff." He said quietly, as he began to empty the contents of his backpack on to the bed. He picked up the clothes and placed them in the closet that was near the bed. He then picked up the laptop, along with two chargers, a wrapped up sandwich and two bottles of water, and took them into the living room. He placed the laptop and chargers on the table and went straight towards the fridge. He placed the sandwich and the bottles on the top shelf.

"My last meal as a free man." He sarcastically commented. While closing the door of the "stocked" fridge, he scanned the room for an available power outlet. Excluding the ones in the kitchen, he found only two available plugs in the living room, and they were all behind the TV. He picked up one of the chargers and plugged it in and connected it to the laptop, which he placed on the small table and turned it on. While the laptop was turning on, he went over to the counter and picked up the phone. He typed in a long number, but he hesitated on pressing the Send button. After he agreed to work for NERV, he requested that he would be the one to tell his soon-to-be-former employer about his new job. Saying it was one thing, but doing was a completely different matter. After several moments of hesitating, he pressed the Send button. He waited for several minutes till someone answered the call.

"O'Donnell's Pub." Said a woman with a Gaelic accent

"Hey Rosie. It's Mark."

'Today is Thursday.' Shinji thought as looked at the calendar. 'That means it's Asuka's meal of choice tonight.'

He took the ingredients out of the fridge and placed them on the counter. As he began to make dinner for his roommates, he looked over his shoulder and saw Asuka going through the channels at an incredible speed. This wasn't different from her usual behavior, but still he could tell that something was different about her. If he didn't knew better, he would swear that she was trying to avoid him or something like that. Pushing that thought aside, he continued to prepare the dinner; unaware that he was being watched by the girl in question.

'Why him?' Asuka thought as she looked at the fellow pilot.

Two days ago, during the medical examination at the hospital, she told Dr. Akagi about her "encounter" with Shinji in the plug. The doctor only made a quick note in her report about it and told that it was mostly likely that her mind tried to fight off the effects of the angels attack. So her mind generated Shinji's image. And that's what was frustrating her for the past two days.

'Why was that pervert there, and not Kaji? Kaji is the only one that is right for me.' Sadness fell upon her. It was 3 weeks since she was told that Kaji is dead, and yet she couldn't stop thinking about him as if he was still alive. She couldn't accept it. That another person that was close to her was taken away. Ever since her mother killed herself, she didn't allow herself to form any kind bond with anyone. Kaji was the only exception. But now that he is dead, it only made her pain worse.

'Just like Mutti, you are gone forever.' She sadly thought. She took another look at Shinji. Looking back, ever since she got here, she used almost every opportunity to insult and belittle him. But he never insulted her. Not even after she tricked him into kissing her and told him that it was horrible. She couldn't understand why he never tried to attack her in any form.

'Maybe it's because he…..' Before she could finish her thought, she heard a familiar sound of a beer can being opened. She looked to her left and saw Misato drinking her beverage of choice while she was looking at in mischievous way.

'Oh mein Gott. How long has she been here?' She though while trying to hide her fear.

"Seeing anything that you like?" Misato teased.

"What do you mean?" Asuka asked, pretending to be ignorant.

"For moment there I could swear that you were checking out Shinji." Misato said before taking another sip of the beer.

"WHAAAAAAAAAAT?!" Asuka yelled so loud that an old couple that was living on the ground level heard her. "Why should I be interested in that pervert?"

"Calm down Asuka. I was only joking" Misato said, while inching away from red-headed time bomb. To her surprise, Asuka only lowered her head and grumbled something.

'Looks like that attack really changed her.' Misato thought as she finished off her bear.

Deep down, in the most vital part of NERV Headquarters known as the Terminal Dogma, soulless bodies drifted inside of a massive tank of LCL. Only a few people knew about the existence of the hidden facility and less knew about its purpose. One of the few people was working frantically on the console. Dr. Akagi typed at the speed that not even she knew was possible. Ever since the Angel attack, the scanners inside the Chamber of Gaff were constantly showing unusual readings. She didn't like working on this project, because it mean working with First Child. She knew what "she" had made her mother do and she could never forgive her for it. But still, she had to do it in order to prove herself useful to Commander. She knew full well how he dealt with those that were no longer useful to him, and she didn't want that to happen to her. Finishing the adjustments on the Chamber of Gaff's systems, she then closed the interface program and left the room.

Several minutes after the blonde doctor left, in the tank filled with numerous clones of the First Child, two bodies touched each other. Suddenly, they both turned around and faced each other. What made these "shells" different from the rest was not only the look on of curiosity their faces, but what was inside their hearts. Through some strange means the two "shells" managed to acquire a soul of their own, and neither of the souls originated from Rei.

Meanwhile…

In a dark and spacious office, two men were looking at reports in several folders that were scattered on the desk.

"Are you sure that this was the appropriate course of action?" Vice-Commander Fuyutsuki asked, while reading one of the reports.

"We have no choice. If the old men got him, it would definitively endanger our scenario." Commander Ikari answered in his usual cold tone.

"Doesn't making him to join NERV also endanger both ours and theirs scenario?" The Vice-Commander asked, placing the report on the desk.

"Don't worry. All is being taken care of." The Commander said as he leaned back in his chair to watch the Tree of Sephiroth on the ceiling.

'Any minute, now.' Mark thought as he looked at his watch. This whole situation was ironic. He left the army, because he felt that he was going to lose his mind on one of the missions, and now he is being dragged into a military organization right after he went "insane".

'Oh, the irony' He thought.

He went to the balcony and watched the sunrise, Due to his insomnia, he spent every morning watching the sunrises. For him that was the true beginning of a day. He has watched a lot of sunrises from different sites in the world and each has had its own beauty, but this one felt different. Before he could finish both his though and enjoying the site, the door bell rang. He picked up his wallet, keys to the apartment and his cell phone, and went to the door. He was greeted by the same men that escorted him to the apartment.

"Sir…" One of agents spoke, but Mark cut him off.

"I know. Let's get this over with." Mark said as he closed the door of the apartment and locked it. The agents lead him to a black SUV and drove of NERV Headquarters.

After 20 minutes of driving around the city, they entered a tunnel in which the SUV was mounted on some kind of train.

"Where does this go to? China?" Mark asked, but neither of the agents answered.

After five minutes, the train left the tunnel and Mark was amazed. The place was huge, it could practically house a city several times bigger than Tokyo 3. He could clearly see a lake, a huge forest, a pyramid with some kind of logo on one of its sides, and something that would appear to be the base. All this was illuminated by the light that was coming from the massive shafts that were on ceiling of this massive cavern.

"My God…" Was all he could say.

End of Chapter 2

A/N – I appreciate and thank for all the support and response that I got for my first chapter. The next chapter will published in a month or two due to the exams that I have.

Pre-read by HaloEvangelion3


	3. Chapter 3

Chapter 3: Plug and Play

By Gesser87

Disclaimer: Read the 1st chapter.

Hundreds of people walked through NERV HQ's main entrance gate. This sight was not unusual in the morning, when the morning shift would arrive. But what made this mornings sight unusual was a bleach blonde woman standing near the entrance gate.

'I always end up being in the "welcoming committee".' Dr. Akagi thought as another group of employees walked by her. 'At least I didn't end up with Kozo's "chore".' She smirked at that thought. The Vice-Commander had to go to a press conference on the Commander's behalf. The conference was about certain claims that NERV went over their jurisdiction during the latest Angel attack. Knowing how the press react to any kind of NERV or Angel related incidents, Fuyutsuki wouldn't be back at Headquarters for at least another 12 hours.

Amongst the small crowd of personnel, she spotted the person she was waiting for. A man, with distinct European features, that was accompanied by two men in dark suits. She slowly walked towards them.

"Mr. Mulligan." She said, getting both Mark's and his escort's attention. As they approached her, she signaled the agents to leave. In a matter of moments, the agents were out of sight. "Follow me, please."

Mark followed her to one of many elevators that were in the lobby. As they entered the elevator, what immediately got Mark's attention was the sheer number of buttons. He could only imagine the size of Headquarters. The elevator slowly began its descent.

"About my job description…" Mark said as he leaned against the elevator.

"Do you know about the Second Impact?" The blonde doctor asked.

"Who doesn't know the day when the world was plunged into Hell?" Mark asked.

"Let me rephrase my question." Dr. Akagi said, causing Mark to cock on eyebrow. "Do you know what caused the Second Impact?"

"If you are about to tell me that the cause wasn't the meteor, that won't surprise me much."

"You are right about it. There was no meteor to begin with." The doctor began, getting Mark's full attention. "The true cause of the Second Impact was an entity that we codenamed Adam. It's 'display of power' caused not only the destruction of Antarctica, but it also shifted the Earths axis."

"My God…" He silently said.

"That's not the worst part. Even though Adam was severely weakened and is currently in sate of stasis, it is still powerful. All it needs is a 'recharge'. That's where Angels come into picture."

"Angels?"

"Beings that are Adam's descendants. Their main objective is to revive Adam and NERV's main goal is to stop them in doing that. That's where your job comes in."

"Which is?"

Before he could hear the answer, the elevator stopped and the doors opened. A small smile formed on the doctor's face, as she imagined his reaction to what she was about to show him.

"You'll know it soon."

*************

A blue car rushed down the parking lot at dangerous speeds. If this happened in a place with a normal working environment, people would make a big fuss out of it. However, since this was happening in the parking lot of NERV's Headquarters, people that were there weren't paying much attention. 50 meters away from the wall, the car started to break and to turn. In a couple of seconds, the car came to a screeching halt just as it entered one of many parking spot. The door of the car opened and a familiar figure of Major Katsuragi stepped out of it. Straightening her jacket, she proceeded to her office.

As she walked down the corridor, she could feel it again; that feeling that something big was going to happen and she was sure that it wouldn't be an Angel attack.

'Maybe it's because of Ritsu's visit last night.' The purple haired woman thought. Recalling the blond doctor's last night visit, Misato could tell that she was hiding something. She couldn't tell what exactly, but she was sure that Ritsuko was not delivering her some sedatives in case if Asuka goes nuts.

As Misato approached her office, she noticed that people were quite busy today. Almost as if they were preparing to perform a synchronization test. She dismissed that thought, knowing that if there was any kind of test that involved the pilots, she would have been among the first ones to know about it.

As she entered the office, the first thing, and perhaps the only thing in her view, was the massive pile of reports and documents that needed to be signed.

'This is officially a crappy day.' She thought as she sat down in her chair. Before she picked up the first report, Misato noticed a memo on the massive pile.

'Probably another one of those staff meeting notices.' She thought as she picked it up and read it. Skipping half of the memo because of techno-babble, she noticed a paragraph in which said that the experiment on Unit 00 was approved.

'That's odd.' She thought. 'Ritsu told me that Unit 00 was not damaged.' Wanting to see what was going on and to get away from the massive pile of papers, Misato got out of her office and went to see the blonde doctor.

*************

"SWEET JESUS!" Mark yelled as he looked at the giant head that belonged to Unit 00. "What the hell is this thing!?"

"Mankind's only weapon against the Angels, an EVA." Dr. Akagi stated.

"How many of these things exist?" Mark said, as he walked closer to the edge of the umbilical bridge.

"Currently, there are 3 active units; 00, 01 and 02. Units 05 through 13 are being produced as we speak." The blonde doctor said, as she looked over some readings that one of the technicians gave her.

"What happened to Units 03 and 04?" Mark asked, as he remembered the image of the red EVA. "Was it the one that I saw a couple of days ago?"

"No. That was Unit 02." Dr. Akagi stated as a matter of fact. "Unit 03 was destroyed in combat, while Unit 04 disappeared during its activation test. I believe that you've heard it on the news several months ago."

"That base in Nevada?" Mark asked, feeling a nasty chill running down his spine. He didn't liked where this was going. "Are you sure that it won't happened with the other EVAs?"

"Unit 04 was fitted with an experimental component that was not present in the previous Units. Therefore it is safe to pilot the Units that are at our disposal." Ritsuko said, while looking at the new pilot. The look in his eyes reminded her of herself, when her mother showed her one of the first EVA prototypes. The look of a child that saw something new and amazing. 'Wait till you see the EVA's true face.' She sadly thought, while maintaining her calm visage.

"Which Unit is this?" Mark asked, snapping Ritsuko out of her dark thoughts. "01?"

"No. This is Unit 00." Ritsuko replied. "Unit 01 has _certain_ difficulties with pilots that aren't designated to it."

"You mean it won't work?" Mark asked, turning his head to look at the doctor.

"Correct."

"Correct me if I'm wrong." Mark said as he took another look at the blue giant. "Doesn't the marking '00' stand for a prototype?"

"It does." Dr. Akagi answered. "But it does the job." The doctor turned around and began to walk towards the cage's exit. "Let's go."

"Go where?" Mark asked.

"To see if you are compatible with this Unit." The doctor said, before she exited the cage.

*************

After 20 minutes of wandering around the Headquarters, Misato finally found Ritsuko's office. Entering the office, she saw Ritsuko's assistant Maya taking some files from her desk.

"Hey Maya." Misato said as the closed behind her. "Have you seen Ritsuko?"

"Sempai is in the Control Room, Major Katsuragi." The young assistant asked. "Is there something wrong?"

"I just got a memo in which it says that Unit 00 is being used in a synchronization experiment." Misato said. "I thought that Unit 00 is in good condition."

"Actually we are running the experiment to see if it's compatible with the new pil-" Before she could finish here sentence, Maya covered her mouth.

"You said WHAT!?" Misato asked the assistant so loud that everyone in the corridor could hear her.

*************

The head of the engineering crew signaled the Control Room that they have finished with necessary alterations to Unit 00's entry plug. As they mounted the pilot's seat in it, a man approached the platform. The engineers were pretty much used to the sight of the 3 EVA pilot's in their plug suits, but to their surprise was not only that new pilot was foreign, he was also a grown man.

"Where do you think they found this one?" One of the engineer's asked.

"Don't know." Another engineer said. "Probably in a lab of one of those hellhole countries."

"Both of you knock it off." Their supervisor said. "You are paid to work, not to comment."

"Yes, sir." Both engineers said in unison, as Mark walked pass them.

Two engineers came from the side and helped Mark get into the plug. Once he entered the plug and he sat in the chair, the head of the crew signaled the Control Room that they could start.

*************

"Mark, can you hear me?" Ritsuko's voice came over the plug's comm system.

"Loud and clear." Mark answered.

"Good." Dr. Akagi said. "Now we are going to fill the plug with LCL and then we'll start the test." Before Mark could say anything, Ritsuko cut him off. "We went through this already. The LCL will supply you with oxygen, so don't bother holding your breath."

"Easy for you to say." Mark said. He began to breathe deeply, so he could saturate his blood with as much oxygen he could.

Before he knew it, the plug began to fill with an orange liquid. He immediately took a deep breath before the LCL liquid covered him. Instinctively, he closed his eyes. This way he could last longer, because he wouldn't have any kind of reminder on how much time has passed.

While the LCL began to cover his ears, he didn't hear the loud entrance of an angry woman, who was accompanied by another woman.

"Ritsuko, what the fuck is going on!?" Misato demanded.

"Misato calm down-" Ritsuko tried to calm down the obviously angry Major, but Misato cut her off.

"Like hell I'm going to calm down. Is this the reason why you brought me those pills last night? To calm down Asuka when she finds out that she was being replaced?"

"No. Do you remember that civilian that was struck by the Angel's attack?" Ritsuko asked.

"Yeah, why?" Misato asked.

"Well, he is that civilian." Ritsuko said. Misato was speechless.

"Sorry Sempai for being late." Maya apologized.

"It's alright." Ritsuko said.

Maya immediately went to the only available console and began to monitor the process.

"Time elapsed?" Ritsuko asked one of the technicians.

"3 minutes and 11 seconds." The technician replied.

"Time from what?" Misato asked. Ritsuko sighed.

"Mark, the new pilot, is instinctively holding his breath. I told him that it's okay to breathe it in, but it's obvious that his instincts are in charge. Until he breathes it in, we can't start the test." Ritsuko said. She turned her head to one of the technicians. "Tell the emergency crew to be on stand by."

At the doctor's last comment, Mark opened his eyes. Realizing what he did, he immediately shut them.

'Crap!' He thought. 'That was the last thing that I needed. It's bad enough that the techs are telling how much time has passed, but opening my eyes was a big mistake, it must have taken at least 10-20 seconds off my maximum time.'

Mark began to have that feeling. The feeling in his lungs that was telling him that he didn't have much time. His choices were obvious.

Keep your breath in and suffer hypoxia, or breathe the stuff in and see what happens.

As the time passed, the second option became more and more appealing.

His body started to slowly become numb. He knew that he didn't have much time.

'Time for the leap of faith.' He thought as he opened both his eyes and his mouth. As the bubbles of air went straight up, he could feel the warm LCL slide down his throat and into his lungs. The sensation of liquid in his lungs made him squirm and turn in his seat. This feeling lasted for several agonizing moments, until the LCL supplied enough oxygen into his blood.

As he took his first breath of LCL, he suddenly felt nauseous.

"Uuuuuuaaaaahh." He moaned.

"How are you?" Ritsuko asked.

"Good thing that I didn't took that beer from the vending machine when I had the chance." Mark said, trying to keep his lunch from going out the same way it came in.

"Do you want us to wait till you feel better?" Dr. Akagi asked.

"Give me a minute or two." Mark said as he placed his hands on his head.

"His reaction is more noticeable than with the other pilots." Maya said, as she made the preparations for the nerve connections. "Could it be because he is an adult?"

"It could be." Dr. Akagi answered. "During the EVA development, there were some cases in which the subjects experienced much worse cases of nausea. It turned out that, compared to children's bodies; adults are slow at adapting to this kind of oxygen delivery system."

"What does that mean to…him?" Misato asked.

"Mark's symptoms are somewhere in the middle range." Ritsuko said as she read the data from Maya's console. "Mark, how are you feeling?"

"Still nauseas, but good to go." Mark said.

"Commencing first connection. Connect main power supply." Ritsuko ordered.

"Main power supply connected." One of the technicians said. "Activation voltage has passed the critical point."

"No problems found in initial contact phase."

"Roger. Shift format to Phase 2." Ritsuko said.

"Connecting pilot to Unit 00."

"Open circuits."

"Harmonics are normal."

"Approaching borderline in 3.1…"

"…2.4"

"…1.7"

"…1.1"

As the technician counted down, some of the other techs in the control room became nervous. The battle with the 13th Angel still fresh in their minds, they began to imagine what would happen if that disaster were to repeat itself.

"…0.9"

"…0.5"

Dr. Akagi slowly approached closer to the thick glass that was separating the Control Room from the cage in which the blue behemoth was held.

"…0.2"

Now, it was the moment of truth. Most staff held their breath.

"Borderline cleared."

The most of the technicians let out a collective sigh of relief. But they immediately returned to their work. Dr. Akagi approached her assistant's console.

"What is sync ratio?" Dr. Akagi asked the brow haired assistant.

"25.7% and slightly fluctuating." Maya said. "This is amazing."

"Mark, can you hear me?" Ritsuko asked.

"Still among the living." Mark replied as his image appeared on the screen. "I was watching the start up sequence on the screen and I thought that I was on LSD or something like that."

Misato finally saw the man in question. The first thing that caught her attention was not only the fact that he was foreign, but he was a grown up man. She then noticed that he had green eyes.

That reminded her of her mother.

"That's from establishing the neural connection. You don't have to worry about that." Ristsuko said. "Now Mark, try to concentrate. We are getting some fluctuating readings."

"Ok." He said as closed his eyes.

*************

"Glados," the first monolith spoke, "we have transferred the resources to the account that you designated and the intel that you provided us is amazing. Now the time has for you to tell us what we should be looking for."

"Very well." Glados spoke. "Are you familiarized with the concept of an exoskeleton?"

Some of the monoliths said "yes", while some said nothing.

"It's basically an armor that can drastically enhance its user's speed and strength." Glados began. "My company managed to produce 3 working prototypes. First one is an armor that can be used for extremely heavy combat conditions. The second one is a power suit that is not armored, but it has stealth capabilities. The third one is a hybrid of the aforementioned skeletons. This was our most promising skeleton. About 7 months ago, their 'users' managed to not only steal the skeletons, but they've also destroyed all the research data; and now we can't build the new ones. That's why I've decided to ask you for your help."

"Wouldn't it be easier if you hired mercenaries or to track them down using their personal data?" One of monoliths spoke.

"They were once trained by the military elite and believe me, they can hide under the radar, but they can't hide from yours. As for their personal data, no success. When they destroyed the research data, they managed to destroy all the data in both the main computer and the back up servers. You can see what kind of situation I'm handling."

"But why are you asking us to help you?" The first monolith asked.

"It's very simple. I am not as influential as you are. I could bet that some of your high level contacts might have noticed some kind of information regarding the renegades."

"Very well. We'll look into it." The first monolith said. "In case our agents capture the renegades, you will give us the technical data on the skeletons."

Glados thought for several moments on should it accept the new term of the deal, while humming the same tune.

"I accept the term." Glados stated. "Now, if you excuse me. I have a meeting to attend to." With that Glados's image disappeared.

"Can Glados be trusted?" One of the monoliths asked.

"For the moment, it seems so." Another one of the monoliths said. "The information that 'he' delivered helped us save some time; and in my opinion, 'he' is a priceless addition."

"So was Ikari." The first monolith said. "We'll continue with the scenario. And we will have to find out Glados's true identity. We cannot allow any further interference with our scenarios."

*************

The LCL from the plug was slowly drained and it was bringing Mark back to the world of gaseous air. As the LCL surface reached his mouth, he tried to breathe in the fresh air. Instead of the feeling of fresh air in his lungs, he felt like he was suffocating. He tried to breathe in several more times before he realized it.

The LCL was still in his lungs. And if he didn't get it out soon, he'll suffocate.

Once the LCL level was beneath his waist, he bent over his waist and coughed the orange liquid out of his lungs. He began to wonder if this will give him any kind of breathing problems. The sudden change of lighting in the plug told him that the plug was opened and that the techs are waiting from him to come out.

"Are you alright?" Asked a technician with a lousy accent, as he looked into the plug.

"Give-e me a-ah….minute." Mark barely managed to say. As he sat there, he noticed that the plug had a very strange scent. Almost like….

"Mark, are you alright?" Asked the blonde doctor, snapping Mark out of his thoughts. "You should get out of the plug and walk. It will help you."

Doing what Dr. Akagi told him, Mark slowly got up and exited the plug. He noticed that both technicians and medical staff gathered around him and Dr. Akagi.

"I'm OK." He said, giving them the thumb up. The medical staff left the platform, while the engineers began to remove the plug from the blue giant.

Mark began to walk towards the changing room with Dr. Akagi at his side.

"I noticed that the changing room has a curtain in the middle." Mark said. "Why is that?"

"When this facility was built," Ritsuko began, "we only had one pilot. And that pilot is female. And due to some budget cuts, we can't construct another changing room for the male pilots. So we used a simpler solution."

"Cut the room in half." Mark said, as they approached the door of the changing room. "Bureaucracy at it's best."

"After you shower and change your clothes, come to the Commanders office. My assistant will guide you." With that, Dr. Akagi entered the elevator and left the EVA cage.

Entering the changing room, Mark sniffed his hand. He remembered this scent. It was the scent that marked some of the darkest moments of his life.

"Blood." He whispered to himself.

He took of his clothes and entered one of the 4 shower stalls. As he showered, the images began to comeback.

A woman with a massive stab wound and the deranged looked of her murderer.

A girl covered in blood, clinging onto Mark's arm; while he was facing a man with a steel pipe.

The burning sensation in his eyes snapped him out of his trance. He quickly rinsed of the shower gel and dried himself. After putting on his clothes, he looked at the locker next to his. Unlike the other lockers, this one had a name plate on it. The words SHINJI IKARI were written in both Japanese and English letters.

"Looking forward to working with you." Mark said as put on his shirt. Exiting the changing room, he almost collided with a short brown haired woman.

"Sorry." They both said at the same time.

The brown haired woman immediately recognized him.

"Mr. Mulligan, my name is Maya Ibuki." Maya said. "I am Dr. Akagi's assistant."

"Oh, yeah. She mentioned that you'll be escorting me." Mark said.

"Please follow me." Maya said as she walked to the elevator.

*************

Inside of spacious office that belonged to Commander Ikari.

"Can it be done?" The Commander asked in his usual cold tone.

"Theoretically, it is possible." Dr. Akagi began. "All we need to do is perform small modifications on the nerve connectors and harmonics. With that we might be able to emulate the Third Child's patterns."

"How long will it take to perform the modifications?" The Commander asked.

"It would take us about 14 hours to do the necessary modifications."

The door of the office slowly opened, revealing both Mark's and Maya's figures.

"You may leave." Commander told Dr. Akagi.

Dr. Akagi nodded and turned around and went to her assistant, while Mark walked towards the Commander's desk.

"Have a seat." Commander said in a tone that border-lined on an order. Taking his 'suggestion', Mark sat down on the chair that was in front of the desk. "I believe that you've been wondering what the true nature of your employment here is."

"Yes, I have." Mark said.

"As you know," Commander began, "the EVAs are mankind's only line of defense against the Angels. Are you familiar with the events that occurred over a month ago?

"No, I am not." Mark answered.

"An Angel overtook one of our EVAs and managed to disable most of the ones that we have at our disposal." Commander said in even and cold tone.

"What?" Mark asked, taken back with both what Commander said and the way he said it.

"And the latest Angel attacked our EVA by trying to influence its nervous system. I am sure that you've felt the effects yourself."

Mark shivered at the recollection of the attack.

"This is the main reason why you were recruited." Gendo said. "To teach the pilots better and more efficient ways of killing both EVAs and Angels."

"Wait a minute." Mark interrupted the Commander. "I never worked on anything like this. How do you expect me to teach them anything?"

"The most efficient way to kill an Angel is hand-to-hand combat. One of your fields of expertise. The second reason why you were recruited is the fact that the Project-E was not the only project that was centered on finding the way to stop the Angels. I believe that you have heard of the Jet Alone project."

"The JA debacle?" Mark asked. "That was front page news."

"Along with Jet Alone project," Commander continued, "there is also the TRIDENT project that is funded by the Japanese Government. These projects, might not have met the expectations as the EVAs have, but they are still powerful. I am sure that you are fully aware that with every major project there is possibility of an information leak"

"So you are saying that there is a possibility that someone might make their own versions of EVAs or JA's?" Mark asked.

"Correct."

Mark scratched the back of his head, as he thought about the things that he said. After several minutes of thinking he made his decision.

"Very well." Mark said. "I'll need the files on all the pilots that are active, along with summarized reports of their missions and visual records of their mission that contain the communications between the pilots and command." He sighed as he turned his head to look at the sight that the large window was showing, not noticing a small smile forming on Commander's face.

*************

The school bell rang, signaling the students of Tokyo-3 high school that its lunchtime.

"Itedakimasu." Kensuke said as he began to gobble down the melon bread he bought from the vending machine.

"You should stop eating that junk." Shinji commented.

"What….are you….talking….about? Kensuke said between his "bites". "This stuff is great. Almost every kid in the school is eating it. Besides, not all of us know how to make those bento meals."

"I tried it once. And I regretted it." Shinji said, unpacking his bento. "Not only that it tasted weird, it gave me a headache."

"Really?" Kensuke asked, raising an eyebrow. "That's something new. And speaking of news, anything new from NERV?"

"If you are talking about that beat-up case, the answer is no, not even Misato found anything new about it."

"Looks like Section 2 trying to keep this in the wraps."

Shinji leaned back and looked around the room. After several moments, his eyes were set on the familiar sight of the blue-haired pilot. It has been almost a year since he met her and still he knew so little about her. He somehow hoped that he'd be able to help her get out of her "shell".

Suddenly, he felt as if he was being watched. He looked around and saw Asuka staring at him. In an instant, she turned around, pretending to be interested into something else.

"What's wrong with her?" Kensuke asked.

"She's been like this for the past couple of days. The doctors say that it's the result of the Angel attack." Shinji said.

"Well, looks like that even the Devil can be hurt." Kensuke said as he opened another bag of melon bread.

*************

Mark entered his apartment holding in one hand 2 bags filled with food and drinks, while his other hand held a couple of thick folders and a small bundle of DVDs.

"He-e-ey, it's just an ordinary day, and it's all your state of mind." He sarcastically said in a sing-song voice.

Placing the folders and DVDs on the table, he went over to the fridge and properly filled it with food and drinks. He then walked over to the coffee table and picked up the laptop.

Suddenly, his cell phone rang.

Placing the laptop on the table, he fished took the call phone out of his pocket. Reading _ROSIE_ on the screen, he immediately answered the call.

"It's me." He said.

"Mark…" Rosie said, clearly distressed. The sound of a siren could be heard in the background.

"Rosie, calm down. Tell me what happened."

End of Chapter 3

Omake:

"Are we there yet?" Mark asked in an annoyed tone.

He let a sigh of relief as he saw one of the agents nodding. They've been circling around the Geo-front for the last 30 minutes, all because the agents didn't want to admit that they were lost. Wanting to get over the whole 'welcome to your new job' routine, he ran into the lobby and hoped that the person was still there.

As he entered the lobby, the only thing that greeted him there was the sight of a woman smashing something what used look like some sort of vending machine. Suddenly, he remembered where he saw this woman. It was the doctor he saw the other day.

"YOU GODDAMN PIECE OF SHIT! GIVE ME MY COFFEE!!!" Yelled the blonde woman, while kicking the remnants of the machine.

"What the hell are you guys putting in the coffee?" Mark asked one of the agents.

A/N – Sorry for the major delay. My graphics card broke down and I couldn't finish this chapter until the card was repaired. Now that Mark is introduced, I can now pay some serious attention to the other characters.


	4. Apology

I'm sorry for the delay of the next chapter. I know that it's been a while since I posted the last chapter of this fic and the next one is way overdue. A friend of mine died, and that left me in a messed up state. The latest chapter is finished and I'm waiting for the proof-reader to correct some minor errors in it.

I would like to thank all of you for reading my (first, and probably not the only) fic. If some suggestions, please PM them to me and I will take them into consideration.


	5. Chapter 4

In Memoriam to Marin Budija

May your soul be at rest

Chapter 4 – Salvageable wrecks / Echoes of the past

By Gesser87

Disclaimer: Read the 1st chapter.

Misato took one last sip of her beer as she took one last look at the clock that showed 06:48. For the past hour, she tried to muster up the courage to do it.

To tell her young charges about the new pilot.

She glanced at the pills that were resting on her night stand.

'This is the one blow that she doesn't need.' She thought.

After several minutes of thinking, Misato concluded that the best moment to tell Asuka will be during the today's harmonics test. Ritsuko will be near, along with her staff and the medication needed to restrain the red-haired pilot. Suddenly, another thought crossed her mind.

'How will Shinji react to all of this?'

Despite the things that the young boy was telling her, it was quite clear that piloting the EVA was taking its toll on Shinji. Misato felt a major sense of dread coming over her, as she remembered the way he reacted when his friend Touji got hurt during the 13th Angel attack.

"Hope for the best, but be aware and prepared for the worst," she silently said. Those words were the last ones that her father said before Adam awoke. Ironically, that was her last clear memory of her father. Even though she remembered him standing over the escape pod before it was launched, she couldn't remember what he said to her before the hatch was closed. She spent the last 10 years trying to remember those words, but to no avail.

Metallic noises came from the kitchen. Misato knew that Shinji was making breakfast. She quickly put on the familiar NERV uniform. Picking up the reports that she had to submit, she placed the pills inside her jacket and exited the room.

Even though he had seen Misato fully dressed in the morning on several occasions before; the sight was so unusual to Shinji that he almost dropped the hot frying pan.

"I have to go," Misato said in a calm manner. "Have some paperwork to do. So I won't be back until the evening."

"Ok," Shinji said.

Misato silently berated herself as she walked towards the door. She knew very well what happened last time when Shinji was left out of the loop. As she stood in front of the door, she remembered the horrifying scream that he had let out when he found out that Touji was the pilot of Unit 03. She turned around and walked back to the kitchen.

"What's wrong Misato?" the young pilot asked.

"Shinji, please sit down," Misato said as she sat down. "There is something that I have to tell you, and it concerns Asuka."

Shinji sat down and listened to his guardian's short retell of the things that happened during the last 2 days. Unknown to them, their conversation was overheard by their redheaded roommate.

*************

20 minutes later

Misato stepped out of her apartment and saw a man leaning against one of the building's support pillars.

"I hope I haven't kept you waiting, Mr. Mulligan," she said, proceeding towards the elevators.

"I'm used to waiting," he said, following her. "And, by the way, call me Mark."

Pushing the call button, she noticed that Mark seemed bothered.

"Wild night?" she asked.

"You could say that," Mark said, with a slight frown on his face. "Before midnight, I experienced 2 major shocks. The first shock was that my apartment in Glasgow burned down, and the second was that _all_ my colleagues are 15 years old."

"Eh?" Misato said, stopping for a couple of seconds. "Your apartment burned down and you are acting like it is not much of a deal."

"Major," Mark began as turned to face her, "there are far worse things that can happen to a person. I believe the Second Impact taught the world that little lesson."

*************

Shinji opened his schoolbag and checked if all of his homework was there. His checking was interrupted by a sudden crashing sound. He immediately ran to the kitchen to see if anything fell of the table or the counter. Seeing that nothing was broken in the kitchen, he began to suspect where the sound originated. A couple of moments later, his suspicions were confirmed when another crashing sound came from Asuka's room.

'She's definitively in a bad mood today,' He thought. 'Maybe it's that time of the month?' A small shiver ran down his spine. Clearly remembering how Asuka was like during her last period, he immediately went to the fridge and took out two small boxes. He placed one of the boxes in his bag, and the other on the counter. He knew that it wouldn't do much against Asuka's anger, but it would take her sights off of him for a short period of time. As he was about to close the fridge doors, he felt a presence behind him. Knowing whose presence it was, he turned around slowly. He saw Asuka standing a couple of inches away from him, and what really scared him was the way she was looking at him. Instead of the usual irritated look she had during her periods, her look was showing of anger, along with several emotions that Shinji wasn't able to interpret. He had a nasty feeling that was telling him that he wasn't going to get unharmed out of this situation.

"Errr..H-here is your lunch." Shinji said, hoping that Asuka's anger would be slightly reduced.

"Who cares about that, BAKA-HENTAI!" Asuka said. Upon hearing that, images of tomorrow's headlines flashed through his mind. Before he knew it, Asuka grabbed his hand and started to drag him towards the apartment's entrance.

"Pick up the damn pace," she said in an irritated tone. "You are slowing us down."

"But…we still have time before the school begins," Shinji said, confused with Asuka's actions.

*************

Dr. Akagi read the results of one of many simulations that she was running for today's synchronization experiment. She knew that all those simulations were showing her a small fraction of the possible outcomes. The idea itself sounded preposterous to her, but she knew that she needed this experiment to succeed. She knew that once the dummy plug system is complete, her usefulness will end. Her mother showed her the true price of that.

She could still remember the massive pool of blood at the base of the MAGI, and the sight of her mother's body in the middle of it. The cold and emotionless look that Gendo gave Ritsuko when he told her that he and her mother were nothing more than colleagues. A small sarcastic smirk formed on Ritsuko's face as she realized a great similarity between her current and her mother's situation.

'Like mother, like daughter,' she thought.

She suddenly remembered how she ended up in this "position." It was right after her mother's funeral. Gendo told her great things about her mother and her work and that he would need someone to take over Naoko's position. Wanting to know the truth behind her mother's death, she accepted the offer without hesitation. As time progressed, she slowly became one of the "big wheels" of NERV machinery. After realizing that the MAGI held no answers about her mother's death, she used her only alternative: the Commander. She tried to exploit what little weaknesses he had, but she ended up being caught in the trap that she had set up.

Letting out a long sigh as she stretched her back, she noticed a folder on a big pile of reports. The only thing that made this folder stand out from the rest was the insignia of NERV Medical Center and titled Mark Mulligan. Picking it up, she glanced through several pages before something interesting caught her eye.

"Carbon, iron and lithium… " she said with increasing interest. Suddenly, the phone rang. Feeling both a little tired from running all those simulations and a bit lazy, she pressed the speaker button.

Her assistant's voice came over the phone. "Sempai, the preparations are complete."

"Alright. I'll be there." Ritsuko hung up.

Before she left her office, Ritsuko wrote down IMPORTANT 7 on Mark's folder.

*************

It had been nearly 30 minutes since Asuka "walked" Shinji out of the apartment and his left arm felt like it was about to pop out of his shoulder. Despite knowing how Asuka can act from time to time, Shinji was still baffled by Asuka's behavior. Under normal circumstances, Asuka's tantrum's would begin by breaking some stuff in her room, followed by a major complaining spree in which she would take several opportunities to belittle him. After that, she would calm down to a point where she would complain to Hikari about her life with Baka-Hentai.

But, lately she seemed…

…different.

Almost like she was trying to make him do something.

Before he could come up with an idea as to what she was trying to do, they arrived in front of a huge building that served as an entrance into NERV Headquarters. Shinji suddenly realized the true reason behind Asuka's behavior.

Their sudden arrival made Asuka feel sad. Deep down, she wished that this "walk" would have lasted a little longer. Or the things that Misato told were some kind of a sick joke. Because if they weren't, this could probably be her last opportunity to have Shinji close to her.

"Asuka," Shinji's voice snapped her out of her thoughts, "did you by any chance overhear what Misato told me?"

Asuka stopped dead in her tracks. Squeezing his fist, she slowly turned to face him. When Shinji saw her face, he realized that before him didn't stood the brave and arrogant pilot of Unit 02, but a person that lost everything. That somehow reminded him of his childhood.

Asuka waited.

She waited for Shinji to act exactly the same way that the other one did in her plug during the Angel attack. After what seemed like eternity, a small fear bean to form in the back of her head. She feared that Shinji was going use this as a chance to ridicule and torment her. In a short span of time, that fear grew in intensity and she reacted the only way that she knew. Her face suddenly went from sadness to that of anger. Before Shinji could react, she turned around and dragged him into NERV.

*************

Maya ran the start up sequences for the entry plug's systems. Even though Dr. Akagi explained everything and assured her of the feasibility of it, Maya still couldn't believe what they were planning to do.

Make Unit 01 accept a different pilot.

The idea itself sounded ridiculous. During the battle with the 14th Angel, "it" refused Rei, who was the "universal" pilot. It seemed that all hopes for making the Dummy Plug System seemed to have vanished. And now, they were trying to make the "Beast" accept a pilot that is completely new to the EVA's. It somehow seemed to be too good to be true.

Despite her skeptical thoughts, she believed in her sempai's work.

The sensation of someone's hand on her shoulder made her relaxed. She didn't have to turn around to know whose hand it was.

"Are all the probes in position?" a female voice asked.

"Yes sempai," Maya answered.

"And the pilot?"

"He is being loaded into the entry plug."

"Good. Notify me when the insertion procedure is complete," Dr. Akagi said while looking at the diagrams from a neighboring console.

Dr. Akagi's hand left Maya's shoulder. That simple act of movement made the young technician feel sad.

'Is this all that we will ever share?' she thought. Maya knew that Dr. Akagi was seeing someone, but she secretly wished that she was that person. As moments went on, a small fantasy formed in her mind. It involved her and Dr. Akagi doing some "research" during the night shift. She was so caught up in her fantasy that she almost ignored a message from the loading crew.

"Sempai, the plug has been inserted."

Dr. Akagi nodded. She went to the massive view screen that gave an impressive view at the restrained Unit 01. After several seconds of looking at the well-known shape of the purple behemoth, the view to it was suddenly blocked by a small window that showed Mark's face.

"Mark, are you receiving us?" The blond-haired doctor asked.

"Loud and clear," Mark answered in a professional manner. "So, which Eva am I riding today?"

"Unit 01," Dr. Akagi answered coldly. Mark immediately remembered what she told him about that unit.

"Haven't you said that no one can pilot it except its designated pilot?"

"That's what the previous attempts have shown. We will try using a different procedure to achieve synchronization."

"Wait a minute," Mark said with a noticeable concern. "Is this thing going to leave me brain-fried or something like that?"

"Don't worry. The worst thing that can happen to you is a strong headache, followed by an intense feeling of nausea," She lied. She knew what the worst possible outcomes were, but she chose not say anything about them. Not because she didn't want to scare him, but because she didn't want to scare her staff. Only a small number of NERV personnel knew about the two greatest EVA-related accidents and it was better to stay that way. The last thing that she wanted was a staff that was afraid or too pessimistic to do their job.

"Alright. Let's get this over with," Mark said, while having a bad feeling about this experiment. The plug began to fill with LCL. Mark bowed his head so that he could face the rising level of the orange liquid. When his face was completely submerged, he took a breathed it in. He firmed his grip on the control yokes as he began to feel the sensation of liquid in his lungs. After an agonizing twenty seconds, the feeling subsided.

"Looks like you are getting used to LCL," Dr. Akagi said.

"Yeah," Mark replied. "But I still have to skip breakfast so that I don't start vomiting."

"Commence neural connections," Dr. Akagi ordered her staff. The image on the view screen was replaced with static. After several seconds, one of the technicians announced that there are no problems with the first contact connections, along with the reappearance of the video link from the plug.

"Proceed to Stage 2," Dr. Akagi ordered. Maya immediately began to type in the sequence for both the modifications to the plugs system and the activation of the probes that were installed throughout the whole plug. "Shift format to Phase 2."

Mark could hear the same sentences that he heard when he was being synchronized with Unit 00. Out of all the voices, he managed to hear the voice that belonged to the young technician that he met the previous day.

"Approaching borderline in 3.4…"

"…2.7"

"…1.5"

"…1.0"

"…0.7"

"…0.4"

"…0.2"

For a moment, Mark's comm line almost sounded like it went dead.

"Borderline cleared."

"All system parameters are within the specified limits."

"What is his sync ratio?" Dr. Akagi asked her assistant.

"21.4%," Maya answered. "Even though it's fluctuating, it's still over 20%."

"Mark, I know I told you this yesterday; but you have to concentrate when you are synchronizing with the EVA's." Ritsuko said. "The higher your synchronization ratio is, the better your control over the EVA will be."

"OK," Mark said. He closed his eyes and took in a deep breath. As he exhaled, small bubbles of air left his lungs.

Dr. Akagi watched as one of the screens on Maya's console began to display a large string of numbers.

'This data…' Dr. Akagi thought. 'This is it. The leverage that I need.' Noticing a reflection in the console's monitor, she turned her head. She saw Misato standing a couple of feet behind her. "Good morning, Misato."

"Mornin'," Misato said as she approached the view screen. Dr. Akagi could clearly see that Misato was worried. Ritsuko tried to ask her if she was alright, but Misato cut her off.

"How long will it take before the new pilot is capable of being sent off into combat?"

"His initial scores were pretty good," Ritsukko began. "And he has military experience, so that will greatly reduce the time required for his training. My estimate is two to three weeks."

"I see," Misato said. "What will happen to Asuka?"

Even though Dr. Akagi expected this question from her friend, but she couldn't give her a sure answer.

"If her scores stop dropping there might be some chances that she will be kept." Though Ritsuko couldn't see how Misato reacted to that statement, she knew it brought a small sense of relief to the purple-haired woman. "Maya, what is his score?"

"26.8%. This is almost identical to the scores with Unit 00."

"Amazing," Ritsuko said. "Mark, how do you feel?"

"Dunno," Mark said as he opened his eyes. "This unit feels…weird."

"Weird?" Dr. Akagi asked. "In what way?"

"Well…" Mark stopped as he took a look behind him, almost like he was trying to see if there was someone behind him. "When I was in Unit 00, it felt like…an oversized suit. But this unit feels completely different. Almost like there is someone in here with me. Also, I can hear some kind of a high-pitched whining sound. Is this typical for this unit?"

When the blond doctor heard this, the idea of the worst possible scenario crossed her mind.

Incompatibility.

If this was the case, the test could end up in failure. And that wouldn't do her any good.

"Do you feel like this "presence" doesn't want you in there?" She asked in calm manner.

"Don't think so. It's more like it's…uhhhh…I don't know. Also, the whining sound is starting to get louder."

Dr. Akagi's mind went through a lot of possibilities as to why this was happening. The whole "presence" issue could mean that Mark is capable to synchronize with the EVA on a completely different level. She would deal with this issue later. But now, she will deal with the more manageable issue.

"Maya, change the phase shift of connectors to 7.6."

Maya typed in the modification.

"Is it better now?"

"No. The whining is still getting louder and the pre…sseeeee−" Mark's eyes suddenly rolled back and his body started to convulse. Consoles started to beep and the technicians started to report all sorts of errors.

"The pulses are flowing backward!"

"Nerve elements activity is increased by 300%!"

"Break connection circuits and eject the pilot!" Dr. Akagi yelled at her assistant.

"Negative! The signal is not being received!" Maya replied. Her eyes widened when she looked at one of the screens. "Mark's sync ratio is 150%!"

"What?!" The doctor asked. 'This can only mean one thing. Mental contamination.'

Before her question got answered, the beeping of the consoles stopped.

"All systems are back to normal," one of the technicians announced.

Dr. Akagi felt slightly relieved that the mental contamination was stopped before any serious damage could have been done. Before she managed to order her assistant to remove the entry plug, two teenagers barged into the control room. Most of the staff was too busy with making sure that purple behemoth didn't go berserk that they didn't noticed the sudden appearance of a redheaded girl with a boy in tow. Misato noticed them.

"Shinji, Asuka, what are you doing here?" Misato asked, but a second later realized the most likely reason.

Asuka released her grip of Shinji's hand and slowly approached the view screen that still showed the live feed from the entry plug.

"Is he…" Asuka began, but stopped for a moment to stop herself from crying. "…my replacement?"

Misato knew how this situation would most likely end. She slowly reached into her pocket and took a hold on a small, orange container.

"Asuka…" Misato began, but Asuka cut her off.

"I WANT A FUCKING ANSWER!!!" Asuka screamed so loud that she got the attention of almost every technician in the room.

"Asuka, please calm down. I'll explain it all later," Misato said as she placed her hand on the girl's shoulder.

Tears started to roll down Asuka's face. From her point of view, her life just ended. They found someone who would replace her and prove that she was a waste of time.

'Was this how Mama felt at the end?' She thought as she remembered the image of her mother hanging from the ceiling. Her thoughts were suddenly stopped by someone's embrace. She tried to look at the person that was hugging her, but her view was obstructed by the person's hair. The faint smell of lavender gave away the identity of this person. She tried to push Misato away, but her body refused to move. She began to feel the warmth from the embrace, and it gave her the feeling of safety.

Shinji stood a couple of feet away and watched them. He was angry at himself. Ever since he met Asuka, he knew that she was proud of the fact that she was an EVA pilot. He knew that the news about the new pilot was going to crush her spirits. But still, he did nothing to either comfort her or make the news be less stressful to her. In the mist of his angry thoughts, he heard a song.

"Hitotsume no kotoba wa yume

nemuri no naka kara

mune no oku no kurayami wo sotto

tsuredasu no"

For a moment Shinji thought he was hearing things, but he realized that it was coming from comm link.

"Futatsume no kotoba wa kaze

yukute wo oshiete

kamisama no ude no naka e

tsubasa wo aoru no"

A male voice sang it in a gentle tone. The words from that sounded familiar to Shinji, almost like he heard those words a long time ago.

"Mita koto mo nai fuukei

soko ga kaeru basho

tatta hitotsu no inochi ni

tadoritsuku basho"

'It can't be,' Shinji thought as he finally remembered where he heard this song. "M-Mother…" He said quietly.

"Signal received. The plug is being ejected," Maya said seconds before the video feed on the view screen disappeared, leaving the young pilot a clear view at the upper half of his unit.

*************

2 days later.

Misato stood on the umbilical bridge, looking at the purple behemoth that was known as Unit 01. She still couldn't stop thinking about the failed experiment. She knew what Ritsuko would say about the mental contamination. She even read about its consequences from the medical files of Asuka's mother. But still, it didn't prepare her for the results of the experiment's failure. Even though Mark was exposed to it for a really short period of time, there were some rumors from the Cranial Nerve Center, rumors that were saying his brain suffered immense damage. Those rumors made her worried about her young charges, because they were the ones piloting with a risk of sharing Mark's fate.

Hearing footsteps, she turned her head towards the docking ramp's door.

"Can't sleep?" the fake blond asked.

"You could say that," Misato replied. "How is Mark?"

Dr. Akagi hesitated for a moment, knowing well what the implications of her answer were.

"The tests have shown that his cranial nerves suffered tremendous stress. We won't be able to know the full extent of the damage until he regains consciousness," the blond doctor said.

"When will that be?" Misato asked.

"I honestly don't know. It could be in a couple of hours or several days or weeks. How is Asuka holding?"

"The news about the pilot really shook her up, but the rumors about Mark's potential 'injuries' made her act like her old self."

"That is natural for her. From her point of view, the person who threatened to take away her meaning of life has been removed."

A cell phone started to ring. Fearing that it might be related to Asuka, Misato immediately took her cell phone and saw it wasn't hers ringing.

"It's me." Dr. Akagi said, holding her cell phone. "When did it happen? Run the basic contamination detection tests. I'll be there as soon as I can." And with that, she placed the cell phone back into her pocket.

"Was that…" Misato began.

"News about Mark? Yes," Ritsuko finished her sentence. "He just woke up. And the it's not good."

*************

1 hour later.

Vice Commander Fuyutsuki walked down the white hallway of Nerve Cranial Center. Under normal circumstances, he would avoid that particular section of the hospital complex. It brought back some unpleasant memories regarding two of his favorite students. The only reason why he came to this facility was a report from one of the doctors. He wanted to see with own eyes that the report bore some truth.

As he slowly approached his destination, he noticed that nurses were running around like they were looking for someone. The sight of a nervous doctor gave him a firm idea as to what happened.

"What happened?" He asked the young doctor in a polite tone.

"W-Well…" the doctor began nervously. "About 20 minutes ago, the patient unplugged himself from the monitoring devices, saying that he is going to the vending machine to grab a snack. And as he approached the vending machine, he…ah…" The doctor paused for a moment, trying to figure out a way to say it without making him look like an incompetent fool. "…We lost track of him."

"So," Fuyutsuki began, "what you are saying is that you let a patient with confirmed mental trauma leave his room. Unsupervised. And as a result of that, he ran away. Am I right?"

The doctor was silent. Not because he knew that he made a great error in judgment, but because he knew that his medical career was most likely over.

"You've recently graduated from the university, right?" the Vice Commander asked.

"Y-Yes, Sir," The doctor quietly answered.

"And this was technically your first patient, right?"

The doctor nodded.

"May I see the files?" Fuyutsuki asked. The doctor immediately gave him a thick folder that held results from all sorts of tests. He scanned several pages before he gave the folder back to the young doctor. "Are you sure that he used the name you wrote in your report?"

"Yes, sir. Initially he seemed to be frustrated that we were called him Mark. So, when we asked him what his name was, he gave us that name."

"I see," the Vice Commander said. "In the future, give your patients enough room to breathe, but not enough to do things on their own."

The young doctor was baffled. He was sure that the Vice Commander was going to chew him out because of his mistake, not give him an advice.

Fuyutsuki walked pass the doctor and went down the same corridor in which Mark was last seen. He paid little attention to the young doctor's calling. He had a meeting with an old friend of his.

*************

She leaned against the guard rail, feeling the gentle breeze. She wondered how long it had been since she felt this sensation. Even though in her head seemed like it was only days ago, she knew that a much greater amount of time had passed.

There were so many things she wanted to see and do, but some things had a greater priority. Her first step was getting out of this hospital. She had nothing against the doctors that worked here, but they treated her like she was a rare specimen.

"Well, that's not far from the truth," she said and immediately scrunched her eyes.

Even though she got most of the facts from the nurses, she was still not accepting the fact.

The fact that she was now in a completely different body.

But that was the least of her concerns. Her biggest concern was escaping the medical complex without drawing too much attention. That was already a big problem considering her body's western features.

"It's been a while, Yui," a male voice came form behind.

Turning around, she saw a tall man whose gray hair clearly gave away his age. His serious posture was contrasted by the gentle look in his eyes.

They stared at each other for several minutes, filled with questions they couldn't and didn't want to answer. Yui decided to break the silence.

"The first thought that came to my mind when I woke up was that I must have botched it up, or that Naoko's fiddling canceled out some of my modifications. But then I noticed that my body was…strange. My arms were hairy and my chest was flat. At first I thought that this was most likely caused by hormonal imbalance that was created by the EVA itself. But then, another thought came across my mind. So, I looked at my…" She paused because she couldn't an appropriate word that could describe her most disturbing change.

"Groin?" the Vice Commander said. Yui's response was a shy nod. He could clearly see that Yui wanted to avoid this subject.

"How is Shinji?" she asked.

The gentle look on the Vice Commander faded away and was replaced by a look of hesitation.

"Shinji is doing well," he stated, "considering his circumstances."

"I see that you still have the habit of sugarcoating the facts when they don't sound favorable."

The Vice Commander let out a small chuckle.

"I see that this whole ordeal hasn't changed you, Yui."

"Well, not entirely," she said, pointing at "her" body. "But seriously, Kozo, how is Shinji? What happened to him?" Her tone changing from playful to concerned.

Fuyutsuki, knowing that he wouldn't be able to change the subject, decided to give her a straight answer.

"Shinji has become one of our best Evangelion pilots. His performance is superior to the other two pilots we have. As for his personal life, he lives with two roommates and he has made some friends. For the moment he seems to be like any other teenager."

"And what about his relationship with Gendo?"

Fuyutsuki stood silent. He knew that Yui wasn't going to like this answer. He looked her in the eyes and was about to tell her, but he saw that Yui started to cry. He found the sight to be distasteful. Even though it was his favorite student standing before him, he always found the sight of men crying to be unpleasant.

"All I wanted to was to make the world safer for him, to make a world in which he would be happy," she said. "I just want to see him, Kozo."

" — I know that, Yui, but think about the way he would react to seeing you in your current condition. It would be..."

"I know," she cut him off. "I know that. But I still want to see him. Please, let me see him."

The Vice Commander took a deep breath. He knew that no matter which choice he made, someone was bound to get hurt by it.

After a short, but careful, consideration, he gave Yui his answer.

*************

Shinji idly flipped through the channels, trying to calm himself down. His usual means of "coping" with everyday stress, his SDAT player, wouldn't work because the batteries were drained. He couldn't go out and buy a new battery pack, because the closest stores were closed and he didn't want to walk for almost an hour to the nearest drug store. So, he decided to do the next best thing, watch TV.

After several anime, history, and movie channels, Shinji's frustration began to slightly intensify. Despite the fact that, for the time being, he had the freedom to choose which channels he was watching, he still couldn't achieve the sensation of comfort that he would feel when he listened to his SDAT. There was another thing he couldn't do when he was watching TV.

Suppress some of the events that were too stressful for his young mind.

His mind began to play back the events that happened two days ago.

What bothered him the most about that incident was not the fact that the new pilot suffered potentially tremendous brain damage, nor the fact that the same thing could happen to him. What bothered him the most was the song that the pilot sang. That same song his mother sang on that fateful test, moments before the EVA consumed her.

He knew that his mother's soul was somehow integrated into the EVA's core. He felt her on two separate occasions and during both times, the only thing he managed to "receive" from her were abstract images that were mostly comprised from the events that he experienced. He could only wonder as to what Mark saw or felt when he synced up with Unit 01.

"Is there anything good to watch?" a gentle female voice asked. Shinji turned around and saw that Asuka was standing right behind him.

"Not really," Shinji said.

"That's no wonder, considering how stupid Japanese TV channels are," Asuka said in her usual annoyed tone.

For the past two days, Asuka's behavior went from that of a completely depressed person to the way she acted before her defeat by the 15th Angel. The only benefit that Shinji was able to notice was the fact that she wasn't trying to insult or making fun of him as often as she used to, almost like she was trying to be nicer towards him.

"So, is there anything new going on at school?" Shinji asked.

"Oh, not much," Asuka said. "Hikari says that your nerdy stooge friend is going nuts because he heard some rumors about the new pilot. I almost feel sorry for him." Letting out a loud yawn, she sat next to Shinji. Shinji offered her the remote, but she refused.

A question formed in the back of his mind, but he didn't know if he should ask her. They spent the next 20 minutes watching some cheesy Korean soap opera before Shinji mustered the courage to ask her.

"Asuka, do you think that new guy is going to be fine? As crazy as this may sound, you, Rei and I face just as great of a chance of ending up like him. What do you think, Asuka?" Shinji closed his eyes in preparation for Asuka's potential retribution.

After a couple of moments, Shinji slowly opened one eye, trying to see what Asuka's reaction was and to prevent getting a black eye. The sigh that greeted him amazed and relaxed him.

Asuka was lying asleep a couple of inches away from him. He felt relieved that she didn't got to hear his question.

'She is beautiful when she is relaxed,' Shinji thought as he looked at Asuka's sleeping form.

After several minutes of looking at her, he decided to cover her with one of the spare blankets. Just as he was about to get up, he felt a gentle tug. Looking down he, saw Asuka holding onto the leg of his pants while mumbling something in German. After several attempts to make her release her grip without waking her up, Shinji decided to stay.

About an hour later, he too fell asleep in front of the TV.

*************

Technician Hideoki Matsuori sat at his console and lazily typed in the activation sequence for the MRI. His usual dedication to complete his job in the shortest possible time was lacking because of his major lack of sleep. For the past two days he has been working round the clock, all on the request of Dr. Akagi.

"How many scans will it take you till you realize that the guy's brain is fried?" he mumbled as the computer showed the status on the MRI's components. Taking another sip of coffee, he reached for the drawer. Opening it, he crabbed a pack of cigarettes, but immediately changed his mind. The last thing that he wanted right now was Dr. Akagi writing a report to his superiors about his non-professional behavior.

Almost as if on cue, Dr. Akagi entered the control room.

"Is the machine ready?" she asked.

"Yes, ma'am," he replied.

The doors of the MRI room opened, revealing a nurse and a man with western features. The nurse guided the man to the small plastic bed that was in front of the machine.

'What the…' Matsuori thought. 'How can he walk around with all those damages?' Hoping that this scan would reveal the secret of Mark's recovery, he remained silent.

After the man lay down on the bed, the nurse fastened him and left the room.

Matsuori activated the MRI. The bed pulled into the machine. Looking at one of the side monitors, he saw that the man was in position for brain scanning.

"Mark, can you hear me?" the technician asked.

"I can hear you," Mark replied. This statement puzzled Matsuori. The first thing that struck him was the fact that Mark spoke in Japanese. Matsuroi clearly remembered when Mark was brought in after the 15th Angel attack, Mark only understood a couple of words and phrases. The second thing he noticed was that Mark referred to himself with "watashi."

'This is definitely getting weirder.,' he thought as the machine began to work.

"Just out of curiosity, do you know where Dr. Akagi is?" Mark asked, again in fluent Japanese. "I haven't had a chance to catch up to her."

Dr. Akagi leaned the small microphone into her direction.

"I am here," the blond doctor said.

"Naoko, is that you?" Mark asked, a little bit confused. "You sound a little different."

"I am not Naoko," the fake blond replied. "I am her daughter, Ritsuko."

"Ritsu-chan? From the way you sound, you sure have grown a lot. How is your mother?"

"Please remain calm for the next 20 minutes. All your questions will be answered after the scan is completed," Dr. Akagi said in a cold and commanding way.

Yui didn't like Ritsuko's response. If this girl was the least bit similar to her mother, it could only mean that she was hiding something. Knowing that she was in no position to demand, Yui closed her eyes and decided to go with the flow.

Twenty minutes later, the computer signaled that the scanning sequence was complete.

"Mr. Matsuori, please copy the data onto this data card and erase all records of this scanning," Dr. Akagi said while placing a small black card on the console.

Matsuori picked up the card and placed it into a small slot located on the side of the console. After he typed in the sequences, two progress bars appeared on one of the monitors. While the progress bars slowly filled up, a nurse entered the MRI room and unfastened Yui from the bed. When both progress bars were full, Matsuori removed the data card from the slot and gave it to Dr. Akagi.

"I appreciate your cooperation, Mr. Matsuori. You can take the rest of the week off," the blond doctor said as she left the control room, leaving the grateful, but still confused, technician to ponder about what had happened to Mark.

Dr. Akagi placed the small black card into the breast pocked of her lab coat as she walked down the corridor. Turning around the corner, she saw Yui sitting in one of the chairs, with a nurse and a security guard by her side.

"With all due respect for your professional opinion, Ritsuko," Yui began, "I think that the 'chaperone' is a little bit unnecessary." The only response she got from the head of Project E was a quizzical expression which reminded Yui of her current condition. "I guess you're right."

"Good. Now please follow me."

"Where are we going?" Yui asked as she got up with her chaperones.

"To the Motorics Testing lab. We need to see if your body's reflexes and movement have been damaged by the 'accident,'" Dr. Akagi said as they went towards the elevator.

"So, how is Naoko? I know that she has to be proud that her daughter is working in the same field of science that she is."

"My mother has been dead for the past ten years," Dr. Akagi said.

"My God," Yui said. "How did she die?"

"She killed herself."

"What?!" Yui said in shock. "Naoko would never do that. She is way too stable to do something like that."

Dr. Akagi said nothing. Yui slowly began to realize that the world changed in more than one way."

"My condolences for your loss," she said quietly.

While her outer appearance didn't show it, the fake blond was in a dilemma of her own. She knew that this "woman" was the main reason why her mother killed herself. She had every right to blame Yui and she wanted to, but somehow she couldn't find the strength nor the will to do so. She simply nodded in response to Yui's condolences.

Moments later, the elevator arrived and they all entered without saying a word.

*************

Fuyutski stood in front of the Commander's desk. In a position he certainly wasn't used to, he managed to hide his discomfort.

"How is the situation?" the Commander asked. Fuyutsuki knew that the Commander got the same reports he received, but Fuyutsuki knew why he asked this question.

"Yui is fine, despite the fact that she had the shock of her life when she saw her new 'body.'" The gray-haired man said.

"I see," the Commander said. "Has Dr. Akagi found any kind of explanation as to how this happened?"

"From what she told me, the most likely reason for the failure was the same reason that made it possible for him to synchronize with Unit 01: his mind."

"In other words, the experiment was fated to fail," the Commander said. Fuyustki nodded in reply. Yesterday's failure was the last thing that the Commander needed. In a single swoop he lost two things that gave him an advantage over SEELE: an adult pilot and the Dummy Plug System that could work on Unit 01.

"Ikari," the Vice Commander began, "you do realize what will happen if the old men ever find−"

"They will never find out what really happened," Ikari cut him off. "They will only receive a report stating that pilot Mulligan suffered a mental breakdown that was caused by the mental contamination from Unit 00."

'Do you really think they will believe that?' Fuyutsuki thought.

*************

Several hours later

Ritsuko took the carafe from the coffee maker, along with a small kitchen towel. She knew that this was most likely going to require pulling an all-nighter and her favorite drink was going to help her get through it. Placing the carafe onto her desk, she took the data card out of her breast pocket.

'What secrets are you hiding, Mark?' She thought as she studied the small black card. She turned on her laptop and placed the card into her laptop's card reader. She walked over to the corner of her office, she moved several small boxes of a larger one. Placing her hand into the holes that were located on its side, she picked up the box and carried it to her desk. Opening the box, she found a triangular device with three concentric circles at its top.

"It's been a while since I used this," she said as she blew some of the dust of its top. The last time that she used this device was during the final stages of Unit 00'ss construction. The device came in handy at finding out small design flaws in the Unit that were hard to detect by any other device. Placing the device on the farther side of her desk, she took a cable from the box and connected the device to her laptop. After several minutes of reinstalling the drivers for the device and adjusting its settings to give her maximum performance, she turned on the device. The circles on the device lit up with a slight hum. A small column of light formed in the center of the circles that went up to the ceiling. After a couple of moments, the column morphed into a translucent sphere with small logo in the middle of it.

Dr. Akagi loaded the file that contained the MRI scans. The circle slowly began to morph into an image of a human. Typing several commands into her laptop, the image cleared up, showing familiar features. Dr. Akagi looked into the box and fished out a small remote control. Leaning back in her chair, she used the remote to look into Mark's "inner workings."

"So, this is what you consider to be porn." A female voice jarred the fake blond from her rest. Turning around, she saw Misato standing in the doorway.

"I wish," Dr. Akagi replied half-heartedly. "These are Mark's MRI scans."

"And? How bad is it?"

Dr. Akagi placed the remote onto her table and accessed the files on her laptop. The screen showed two images.

"The image on the left is Mark's MRI scan after the Angel attack," Ritsuko began, while pointing the image on the screen. "It shows pretty much normal brain activity, while the image on the right was taken several hours ago," Ritsuko paused as she pointed to the image on the right, this image had a lot more red colors than the previous one. "and it shows much more erratic activity."

Misato knew that this wasn't good, but she didn't understood what her blond friend was talking about. "The closest example to Mark's brain activity is that of a schizophrenic person."

Misato was shocked at what Dr. Akagi just said. Realizing that her blond friend used the word schizophrenic, she remembered one similar EVA-related incident.

"Is…this what happened to Asuka's mother?" Misato asked. Dr. Akagi nodded. The worst possible scenario crossed her mind. "W-Will he ever recover from it?"

"It's hard to say. The only difference between his case and Dr. Sohryou's case was that Dr. Sohryou lost her grip on reality while Mark ended up with a…different personality."

"Different personality? What do you mean?"

"When he was asked for his name, he replied that his name was Yui Ikari."

It took a couple of seconds before Misato remembered who's name that was.

"What? You are saying that Mark is claiming that he is Shinji's mother."

Dr. Akagi knew that it sounded crazy, but she maintained her serious expression.

"Under normal circumstances we would declare that he is insane, but he said some things that only Yui Ikari would know."

"Like what?" Misato asked.

"That information is classified. And I personally believe that it's better that you don't know."

Despite knowing that her friend was trying to protect her, Misato didn't approve the way Ritsuko was doing it. It was almost the same as the time when Shinji was consumed by the 12th Angel.

"Overall, despite the fact that he has a completely different personality, Mark's body has somehow managed to retain its impressive physical responses," Ritsuko said encouragingly . That had very little effect on the purple-haired woman.

Picking up the remote, Dr. Akagi zoomed in on the holographic image. The bluish image showed a mass that held some sort of lines.

"What is that?" Misato asked.

"The second reason why I wanted a detailed MRI scan of his body. All the tissue samples that were taken from him showed increased concentration of certain elements."

"What elements?"

"Carbon, iron, and lithium. These elements are normally present in the human body, but Mark's body has them in much greater concentrations, yet his body works fine."

Misato was confused. She knew that lithium had an effect on the brain and that iron and carbon were two of the fundamental elements in the human make-up, but she couldn't see a reason why Ritsuko would make such a fuss over it.

"So, he has some extra elements in his body. Maybe he got it from a vitamin pill or something like that," Misato said.

"No," Ritsuko said while shaking her head. "It wouldn't explain the concentrations that he has, it most certainly wouldn't explain the way they are placed through out his body." She pointed at the lines. "It just doesn't make any sense."

"When was the last time anything here made any sense?" Misato asked.

*************

Yui sat on the window board and watched the marvelous sights of Geofront. Even though that there was very little light coming from the huge shafts on its ceiling, it was still a sight to behold. To her, it seemed that just yesterday the whole place was under construction. It was almost like she made a small leap forward in time. The reality was not only different, but also crueler. She knew that she missed out on a lot of things. And one of those things was her son's life. Before she had undergone that experiment, she always dreamed about her son's first day at school, his first friends, his first date, graduation day, his wedding, and her grandchildren. She thought that by doing the things she did, she would somehow make it all possible for Shinji to experience without her presence.

The things that Kozo told her broke her heart. Gendo, her husband and the man that she loved, abandoned their son like a useless thing only a couple of days after she was consumed by Unit 01. And now, he was using Shinji like a pawn in some kind of perverted chess game. And for what? To give the humanity a way out if it's evolutionary "dead end"?

Tears started to flow down her face.

'This isn't the world I wanted for him,' She thought. 'All I wanted was a world in which you could be happy, Shinji.' She brought her hands up to wipe away the tears.

Suddenly, she felt heat all over her body. Moving her hands away, Yui saw that she was in some kind of a village that seemed to be located in the middle of a desert. The houses seemed to be a little bit futuristic and seemed to "blend" with the environment. The thing that made this image odd was that there were no visible signs of people inhabiting the village. She tried to move, but her body simply refused to respond. ALL of a sudden, one of the houses exploded. A solider, clad in a grey armor, ran from one of the remaining houses.

"Shit man!" he yelled, "They blew up the supply house!"

"Calm down," a voice said, which Yui recognized as the voice of her current body. "Tell Sheep, Aja, and Raimundo to get the locals and the package into the basements. Once they are done, they are to defend the southwest side. I will go to the east side, while you will go to the north side."

"Yes, Sir," the man replied with renewed confidence.

"Crap." His voice spoke again, this time with a small hint of Gaelic accent. "Just when things started to look up…"

Suddenly, Yui found herself lying on the hospital floor. Her body shook as she stood up.

"W-What was t-that?" She asked, while staggering towards the hospital bed.

Before the night ended, Yui experienced another hallucination.

*************

Next day

Gendo patiently waited in front of the doors, causing a small commotion amongst the staff. The Commander rarely came to this center, and it was only when Rei Ayanami was hospitalized. But today, he stood in front of the room of the man who claimed to be his late wife. He could hear the faint whispers from some of the nearby nurses.

"_Has he ever gotten over her death?"_

"_Do you think he will try to do 'those' things with him?"_

"_He'll make the guy suffer for of it."_

He paid little attention to their gossiping. What mattered to him was that he, in a way, was reunited with Yui. After seeing the nurse leave the room, he waited for several minutes before entering the room. Gendo saw the man that he, several days ago, "persuaded" to join the organization. Unlike that time, the man's eyes held a different look, the look that Gendo hadn't seen for almost 13 years.

"Well, Gen-chan," the man began, with a small smile, "now you can say that you saw just about everything."

Gendo tried to say something, but the only word that came out of his mouth was his wife's name.

"Yui…"

Yui walked over to the hospital bed and sat on it. Her smile faded away and it was replaced by a more serious look.

"Why did you do it?" she asked. Gendo knew what she was asking.

"When he was near me, all I ever did was cause him pain," Gendo replied in a firm, but gentle tone. "So, I decided that it would be better if I didn't interfere with his life."

"Not interfere?" Yui asked, completely shocked at her husband's answer. "And right now, you're not hurting him with your actions?"

"That only proves my statement."

"You abandoned him when he needed you the most."

Gendo turned his eyes just enough so that he couldn't look her in the eyes. Yui noticed and tried to get up and get his attention, but the sudden feeling of nausea prevented her from doing so.

"Are you all right?" Gendo asked as he helped her get up.

"It's this body," Yui answered. "I think it's rejecting me."

They looked at each other for several minutes, trying to come up with a subject that didn't involve a loud argument. After several minutes, Yui broke the silence.

"Do you think they are wrong?" She asked.

Gendo knew what she meant, but he chose not to answer, out of fear that one of SEELE's spies might be listening in on their conversation.

End of Chapter 4

AN – As you all noticed, my friend died. He was a good friend that helped me get over certain difficulties. In honor of his memory, I dedicate this entire fic to him.

This chapter is finally done. I still have at least 7 chapters to do before I complete this fic. Along with writing the 5th chapter, I will also rewrite the previous 3 chapter. It won't be a major overhaul; I'll simply remove some errors and make certain sentences more understandable. Please, PM me if you have any comments, critics and suggestions.


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